Aspects of a method and system for command interface protection to achieve a secure interface are provided. A host device may encrypt a command based on a key index generated within the host device, a host device key, a command count, a random number from a slave device, at least one host control word, and a host variable value. The encrypted command may be communicated to the slave device where it may be decrypted based on the key index, the host device key decrypted from a slave device key generated by the slave device, the command count, the random number, at least one slave control word, and a slave variable value. The key index may be utilized in the host and slave devices to select a master key from a key table from which generational derivatives may be generated for command encryption and decryption respectively.